How can I highlight PDFs?
In windows, I can use Foxit but on Ubuntu x64, what can I use? Foxit seem to only provide a i386 version
Try http://www.mendeley.com/. They have a nice client with a reader that can annotate, and it's great for organizing your PDFs as well.
You can install the 32bit foxit on 64bit ubuntu by running the command
sudo dpkg -i --force-architecture <name of the file>.deb in a terminal in the same folder as the .deb file.
In such a way, you will not lose the application you are familiar with and you won't have to endure running it through wine either.
Note: the linux version of Foxit does not support text highlighting!